After stealing clothes from a dead Resistance fighter, Marcus makes his way through the desert which was once the San Fernando Valley and comes across the ruins of Los Angeles. While wandering through the desolate and abandoned city, Marcus comes across a T-600 Terminator, which tries to shoot him down. He is rescued by a teenage boy Kyle Reese (Anton Yelchin) and his young, mute, child companion named Star (Jadagrace Berry). After rescuing Marcus, Kyle explains how Judgment Day happened as he knows it, and that he is working to become a full-fledged Resistance member. They lead Marcus back to their home, which is in what is left of Griffith Observatory, where they spend the night. Marcus, determined to help, fixes an old shortwave radio which, by chance, picks up the broadcast from John Connor, whose daily broadcasts are secretly focused on finding Kyle, his future father.
As Marcus, Kyle, and Star leave L.A. to find John Connor, they are spotted by a scout, which recognizes the face of Kyle Reese. They destroy the machine, and make it to an apparently abandoned gas station. At Connor's base, the machine activity in L.A. is noticed, and they deploy air support to investigate. Kyle, Star, and Marcus meet the inhabitants of the gas station, who are trying to avoid detection from the machines rather than fight back. As their leader shares some food with Star and Kyle, they come under attack from a large machine, reaching in and taking live prisoners. After managing to escape the station and being pursued by moto-terminators, the three of them are attacked by a Hunter-Killer (HK) on a bridge, which takes Kyle and Star alive, leaving Marcus behind. The air support Connor sent observes the abductions, but are unable to stop the prisoner ship. They are able to let Connor know what is happening before one is shot down and the other pilot, Blair Williams (Moon Bloodgood), ejects. She is found by Marcus, and they begin to travel to Connor's base.
Meanwhile, John and Barnes test the frequency, and it seems it successfully shuts down Skynet robots. John is determined to discover why Skynet is taking human prisoners. Blair and Marcus bond over the two-night trek back to her base, after he saves her from a gang of rapists and thieves. After detonating one of the magnetized mines surrounding Connor's base, Marcus is revealed to be of machine origin himself, though he was previously unaware of it. However, there is a biological system within his endoskeleton, previously unknown to the Resistance, but later revealed to be the prototype for infiltration terminators like the T-800. During the interrogation with Wright, John learns that Kyle Reese is among the prisoners captured from L.A. Basin.
Blair, unable to accept that Marcus is part of Skynet, releases him from captivity. Marcus manages to elude the resistance members searching for him; however, Blair is captured and he comes face to face with John after saving him from a Hydrobot. Reaching a shaky truce, Marcus agrees to enter Skynet Headquarters and find a way to shut down their defenses so that John and the resistance can attack.
John gets into a heated argument with Ashdown, asserting that the attack would result in the deaths of hundreds of prisoners, and also since Kyle Reese is among the prisoners in the Skynet base, destroying the base would keep John (and thus, the majority of the Resistance) from existing. Ashdown angrily relieves John of his command in the Resistance, but John's followers remain loyal to him. Before leaving, however, John sends a radio broadcast to the Resistance cells, stating that if they go through with this attack, they would be making a cold and calculated strategic attack, thus being no better than the machines themselves. Shortly afterward, he leaves, his wife Kate asking what she should tell his men when they find out he's gone. To which he replies "I'll be back "(quoting the terminator he met from Terminator 2). Ashdown discovers that the Resistance refuses to assault the Skynet compound unless ordered to do so by John. John meanwhile hi-jacks a Moto-Terminator and drives it to the edge of the Skynet base. Marcus inside deactivates the outer turrets and uploads a map to John, who starts his infiltration. He is able to gain entry and release the locks on the prisoner cells, and calls in air support from his base to extract the prisoners. The signal that is leading him to Kyle Reese's cell continues to pulse.
Meanwhile Marcus' machine circuitry syncs with the mainframe, which reveals details of his execution, the death of Dr. Serena Kogan, the United States Air Force's takeover of Cyberdyne Systems' patents, Judgment Day, and ultimately his true purpose and machine programming. Skynet, under the guise of Dr. Kogan, tells him that he was meant to be the perfect infiltrator, whose intent was to lure John to come and save Reese. Unknowingly fulfilling the mission, Marcus watches helplessly as John is ambushed by a T-800, a Model 101 (Arnold Schwarzenegger (CGI) and Roland Kickinger), instead of finding Kyle. Marcus rips out his CPU, insisting even though he's no longer human, he isn't a machine, and swears vengeance toward Skynet for his transformation.
John runs into Kyle and Star, who are fleeing a T-600, which is destroyed by the T-800 following John. The three of them blast through a wall, finding many more T-800s in various states of construction. They also find the nuclear power cells that will be installed. After the T-800 catches up, John sends Kyle and Star away on an elevator to make sure they survive. Marcus joins with John to battle the T-800 on the production floor for Terminators. While the T-800 is preoccupied with Marcus, John rigs explosives to the nuclear power cells. Marcus is punched in the heart by the T-800 and falls to the ground. The T-800 refocuses on John. During the fight John blasts a hole in a cauldron and hot liquid metal falls on the T-800(similar to T2). The T-800, now glowing red hot, manages to get back up. John then shoots open a steam pipe that cools the T-800 and causes the T-800 to slowly freeze. As it is freezing the T-800 reaches out and scratches John's face(matching the scars shown by Michael Edwards' portrayal of John Connor in the intro of Terminator 2: Judgment Day). John goes over to Marcus and starts to pound on his heart in an attempt to start his heart. The T-800, while damaged, gets back up and heads towards John and Marcus. John uses two hot electrical wires to jump start Marcus's heart. As they make eye contact John is stabbed through his chest with a piece of metal. Marcus breaks the metal and uses it to severe the T-800's head.
Sometime in between the above scene, an HK closes in on the Resistance submarine. Moments before the submarine is destroyed, Ashdown realizes that the frequency was part of a Skynet plot to track the submarine and other hidden bases.
Once they are airlifted from the blast site, John detonates the explosives destroying Skynet Central in San Francisco and falls unconscious. Back at base camp, Marcus resolves to give up his heart to save John, providing closure to his story arc at the beginning. He tells Blair that everyone deserves a second chance, and Marcus' was to give up his own heart to save John's life, thus an opportunity of redemption from his murderous past.
After the successful heart transplant, John, Reese and the rest of his team are airlifted out via helicopters from the aid station. John is heard over radio stating, a battle has won but the war continues and "there is no fate, but what we make."
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